Understanding the sources areas and transport mechanisms of pollen grains is important for reconstructing vegetation and climate from fossil pollen data. We studied the modern pollen assemblages of 28 surface samples from different geomorphic units (mountains, the central basin, and the riverine zone) in the Yinchuan Basin in China. Our aim was to compare the characteristics of the pollen assemblages from the different sedimentary environments and to determine the differences in pollen source areas and transport mechanisms. The results show that: (1) The pollen assemblages from the mountain and piedmont alluvial fan environments were dominated by trees, with the tree pollen content decreasing with decreasing altitude. The pollen in the piedmont alluvial fan environment was mainly transported by surface runoff, and assemblage combines the characteristics of both the mountain and the local vegetation. (2) The pollen assemblages from the central basin were dominated by pollen produced by the zonal desert-steppe vegetation. (3) The pollen assemblages from the riverine zone were dominated by a long-distance component from within the upper part of the drainage area. The results suggest that in sedimentary pollen records from the Yinchuan Basin, the arboreal pollen component primarily reflects vegetation changes within the surrounding mountains; the herbaceous pollen component is an indicator of changes in desert-steppe vegetation; and the long-distance fluvially-transported pollen component reflects vegetation changes in the upstream drainage area.